08FBDT00-2019-F-0071 Fiscal Years 2019-2023 Maintenance Dredging Suisun Bay Channel Project.pdf

United States Department of the Interior

FISH AND WILDLIFE SERVICE

San Francisco Bay-Delta Fish and Wildlife Office

In reply refer to:

08FBDT00-2019-F-0071

Ms. Tessa E. Beach Chief, Environmental Section B U.S. Army Corps of Engineers 450 Golden Gate A venue, Floor 4 San Francisco, CA 94102

650 Capitol Mall, Suite 8-300 Sacramento, California 95814

FEB 18 2019

Subject: Biological Opinion for the Fiscal Years 2019-2023 Maintenance Dredging of the Suisun Bay Channel Project, Solano and Contra Costa Counties, California

Dear Ms. Beach:

This letter is in response to the U.S. Army Corps of Engineers' (Corps) December 18, 2018 request to initiate formal consultation with the U.S. Fish and Wildlife Service (Service) on the proposed Fiscal Years 2019-2023 Maintenance Dredging of the Suisun Bay Channel Project (project) within the Federal navigation channel of the Suisun Bay and New York Slough, Solano and Contra Costa Counties, California on the threatened delta smelt (Hypomesus transpacificus) and its critical habitat. Your letter and associated biological assessment were received via email on December 18, 2018 and via postal mail on December 20, 2018. This response is in accordance with section 7 of the Endangered Species Act of1973, as amended (16 U.S.C. 1531 et seq.)

(Act).

In reviewing this project, the Service has relied upon: (1) the Corps' December 18, 2018 initiation letter; (2) the Corps' December 2018, Biological Assessment Fiscal Years 2019-2023 Maintenance Dredging of Suisun Bay Channel; and (3) other information available to the Service.

The Service has reviewed the proposed project and its effects to the delta smelt's designated critical habitat. In designating critical habitat for the delta smelt, the Service identified the following Primary Constituent Elements (PCEs) essential to the conservation of the species:

PCE # 1 is physical habitat for spawning. Reduction in overall spawning substrate is not expected to occur. The reduction is not expected because dredging will be conducted at depths deeper than the known spawning habitat of delta smelt (i.e. shallow water habitat).

PCE #2 is suitable water quality for all life stages. Water quality in the action area will be temporarily affected by mechanical clamshell dredging and by sediment disposal activities at the SF-16, in-bay disposal site. Maintenance dredging of the navigation channel may affect water quality surrounding the area being dredged through the creation of the sediment plumes. The sediment plumes are temporary in nature and typically dissipate within the same day of activity.

Sediment plumes are also discountable in size in relation to the Delta, and would not be expected

Ms. Tessa E. Beach 2 to affect the overall water quality of the Delta ecosystem. In-bay disposal adjacent to the channel is beneficial over other forms of disposal by not removing sediment from the Delta.

PCE #3 is river flow. The proposed project does not permanently divert water out of or away from the surrounding aquatic environment and therefore is not expected to diminish river flow.

However, dredging and shipping channel maintenance increase water depths and increase water supply demands needed to maintain the low salinity zone in Suisun Bay.

PCE #4 is salinity for rearing. The proposed project is not expected to have any significant effect on salinity, since the river flows will not be affected, thus not affecting the position of X2.

The Corps letter requested formal consultation; however, based on the above analysis and consistent with previous consultations on Suisun Bay maintenance dredging, the Service believes that the proposed project is not likely to adversely affect the delta smelt's critical habitat. The remainder of this document represents the Service's biological opinion on the effects of the project on the delta smelt.

CONSULTATION HISTORY

December 18, 2018 The Service received the Corps' initiation letter and biological assessment via email.

BIOLOGICAL OPINION

Description of the Proposed Action

The Corps proposes to conduct annual maintenance dredging of the Federal navigation channel in Suisun Bay, hereinafter referred to as the Suisun Bay Channel, from 2019-2023. The Suisun Bay Channel consists of several reaches, from west to east: Bulls Head Channel, Suisun Bay Main Channel and New York Slough. Table 1 provides the dimensions of the Bulls Head Reach, Suisun Bay Main Channel, and New York Slough. To maintain the channel at a depth of 35 feet mean lower low water (MLL W), up to 200,000 cubic yards is proposed to be dredged annually for five years from a maximum of 15 acres of the Suisun Bay Channel and placed at the Suisun Bay Disposal Site (SF-16). This site extends parallel to the channel for approximately 4,000 feet and is approximately 200 feet wide (18 acres). Maintenance dredging will be conducted using a clamshell dredge.

T bl 1 D' a e : 1mens1ons o u s ea eac , UISUD fB II H d R h S ' ay am B M. Ch anne, an ew or 002 d N Y kSI b

Navigation Length Width Depth Area Channel (feet) (feet) (feetMLLW) (acres)

Bulls Head Reach 2,600 300 39 (35 + 4) 18

Suisun Bay Main Channel

(from Bulls Head Reach 22,400 300-600 35 558 to New York Slough)

Ms. Tessa E. Beach

New York Slough 23,200 400 35 212

Clamshell Dredging

A mechanical clamshell dredge consists of a crane mounted on a floating deck barge, with a clamshell bucket on the end of the crane boom (Figure 1). The deck barge has two to four spud piles attached to the platform, generally at the comers. The spud piles are long pipes that are driven vertically into the bay bottom by hydraulic assistance; they are used to anchor the dredge barge. Clamshell dredges are not self-propelled so they require a tug boat to tow or push the dredge to and from dredge sites.

Figure 1: Schematic of Clamshell Dredging Operations

Once a tug moves a dredge into place, the spuds are driven into the bay bottom anchoring the dredge. The clamshell is raised from and lowered to the channel bottom using a system of cables and winches; the system is powered by a diesel generator. Under its own weight, the clamshell falls through the water column into the shoaled sediment in the channel. The cables restrict the clamshell from going too deep, or beyond the maximum allowable dredge depth. The clamshell then closes and is pulled up through the water column to above the scow. Once over the scow, the clamshell opens and deposits the dredged material into the scow. When the scow is full, it is transported to the dredged material placement site (SF-16) by tugs. When at the site, the doors at the bottom of the scow open and dredged sediment falls through the scow doors to the bottom of the placement site (Figure 2). As material falls through the water column, some sediment is stripped from the descending plume creating turbidity around the scow; however, most sediment falls to the bottom of the placement site.

.. XO\'/

_:.~- At!'.t~!:~!tl:> /-~---, (HlghDensityM.lto • • • • • • ·• · • Dispersion i>Ol>tlooolOreo M.iteflalMoond

(lmpactaoudl

BottomFfow (DensityTranspon)

Figure 2: Aquatic Placement of Dredged Material

When all the material within reach of the clamshell is dredged, the spuds are raised and the tug transports it to the next area requiring dredging. The process is repeated until all material is dredged from the channel. Following dredging, hydrographic surveys are conducted to ensure that the entire area is dredged to the desired depth.

4 .

The maximum daily rate of clamshell dredging is about 7,000 cubic yards per day if operated continuously for 24 hours. Crew changes, moving the dredge from site to site, and other activities (e.g., breakdowns) limit the amount of dredging that occurs, so the effective work time (the time the dredge is actually digging shoaled material) is typically 12 to 16 hours per day. Based on a 12-hour work day, the proposed action is expected to require up to 60 days to complete.

All dredged material will be placed in accordance with the 1999 programmatic biological opinion and amendment on the Long Term Management Strategy (LTMS) for the placement of Dredged Material in the San Francisco Bay Region, California (Service File No. 1-1-98-F-62 and 1-1-04- F-0199).

Sediment sampling and testing of dredged material is also a component of this project. Sampling and testing for the project is on a 5-year cycle, with the next episode scheduled for 2019.

Conservation Measure

• All dredging will be accomplished during the Service's recommended in-water work window for delta smelt August I st to November 30th

Action Area

The action area is defined in 50 CFR §402.02, as "all areas to be affected directly or indirectly by the Federal action and not merely the immediate area involved in the action." For the purposes of the effects analysis, the action area encompasses both the dredged reaches of the navigation channels and the aquatic disposal site. The action area is approximately 33 acres (15-acre dredging footprint and 18-acre disposal site). The Suisun Bay Channel is located in the Suisun Bay and New York Slough, approximately 30 miles northeast of San Francisco, in the counties of Contra Costa and Solano. The action area includes waters of the Suisun Bay and New York Slough navigation channels and the adjacent surrounding waters of Suisun Bay, Honker Bay, Carquinez Strait, New York Slough, and the very downstream portion of the San Joaquin River (Figure 3).

Map Legend

- Su11ur, Bl'I \I Channel

- SF -16 Pb1C1:1menl Sile

- ~~--=· Mlle9 • 25 5 N

Suisun Bay Mein Channel

Figure 3: SBFNC and aquatic disposal site SF-16

Analytical Framework for the Jeopardy Determination

Section 7(a)(2) of the Act requires that Federal agencies ensure that any action they authorize, fund, or carry out is not likely to jeopardize the continued existence oflisted species. "Jeopardize the continued existence of' means to engage in an action that reasonably would be expected, directly or indirectly, to reduce appreciably the likelihood of both the survival and recovery of a listed species in the wild by reducing the reproduction, numbers, or distribution of that species

(50 CFR § 402.02).

The jeopardy analysis in this biological opinion considers the effects of the proposed Federal action, and any cumulative effects, on the range-wide survival and recovery of the listed species.

It relies on four components: (1) the Status of the Species, which describes the range-wide condition of the species, the factors responsible for that condition, and its survival and recovery needs, (2) the Environmental Baseline, which analyzes the condition of the species in the action area, the factors responsible for that condition, and the relationship of the action area to the survival and recovery of the species, (3) the Effects of the Action, which determines the direct and indirect impacts of the proposed Federal action and the effects of any interrelated or interdependent activities on the species, and (4) the Cumulative Effects, which evaluates the effects of future, non-Federal activities in the action area on the species.

Status of the Species

Legal Status

The Service proposed to list the delta smelt as threatened with proposed critical habitat on October 3, 1991 (Service 1991). The Service listed the delta smelt as threatened on March 5, Ms. Tessa E. Beach 6

1993 (Service 1993), and designated critical habitat for the species on December 19, 1994 (Service 1994). The delta smelt was one of eight fish species addressed in the Recovery Plan/or the Sacramento-San Joaquin Delta Native Fishes (Service 1996), and a revision addressing delta smelt is currently underway. A 5-year status review of the delta smelt was completed on March 31, 2004 (Service 2004). The 2004 review concluded that delta smelt remained a threatened species. A subsequent 5-year status review recommended uplisting delta smelt from threatened to endangered (Service 2010a). A 12-month finding on a petition to reclassify the delta smelt as an endangered species was completed on April 7, 2010 (Service 201 Ob). After reviewing all available scientific and commercial information, the Service determined that re-classifying the delta smelt from a threatened to an endangered species was warranted but precluded by other higher priority listing actions (Service 2010c). The Service annually reviews the status and uplisting recommendation for delta smelt during its Candidate Notice of Review (CNOR) process. Each year, the CNOR has recommended the uplisting from threatened to endangered.

Electronic copies of these documents are available at http://ecos.fws.gov/docs/five_year_review/doc3570.pdf and http://www.gpo.gov/fdsys/pkg/FR- 2013-l 1-22/pdf/2013-27391.pdf (Service 2010a; Service 2010b; Service 2012b; Service 2016).

Description and Life Cycle

The delta smelt is a small fish of the family Osmeridae. It is endemic to the San Francisco Bay Delta where it primarily occupies open-water habitats in Suisun Bay and marsh and the Sacramento-San Joaquin Delta. The delta smelt is primarily an annual species, meaning that it completes its life cycle in one year which typically occurs from April to the following April plus or minus one or two months. In captivity delta smelt can survive to spawn at two years of age (Lindberg et al. 2013), but this appears to be rare in the wild (Bennett 2005). Very few individuals reach lengths over 3.5 inches (90 millimeters [mm]).

Population Numbers

The 2018 California Department of Fish and Wildlife (CDFW) Fall Midwater Trawl (FMWT) Index was 0, the lowest on record after the previous record low of2 in 2017. The CDFW Spring Kodiak Trawl (SKT) monitors the adult spawning stock of delta smelt and serves as an indication for the relative number and distribution of spawners in the system. Last year the 2018 SKT Abundance Index is 2.1, the second lowest on record. The 2019 SKT is in progress and results are pending.

In 2016, the Service began calculating an absolute abundance estimate utilizing January and February SKT catch data. The data for each of the previous years was used to calculate a range of estimated adult spawner abundance for that year. 1 This calculation was modified in 2017 and resulting ranges and point estimates are shown in Table 2.

The 2018 absolute abundance estimate is the second lowest following 2016. The January through February 2016 point estimates were the lowest since the SKT survey began in 2002 and

I The Service completed a revised adult delta smelt abundance estimation procedure based on CDFW's SKT data for January and February (see Table 2). This procedure has been updated from that used in 2016. While these estimates likely represent a minimum population size due to the method reliance on survey data, this is our current best estimate of the annual population size, and the actual delta smelt spawner population during January and February of any given year likely fell within the upper and lower confidence interval for that year identified in the final column above.

suggested delta smelt experienced increased mortality during the extreme drought conditions occurring during 2013-2015. While the estimate increased slightly in 2017, it fell again in 2018.

The continued low parental stock of delta smelt relative to historical numbers suggest the population will continue to be vulnerable to stochastic events and operational changes that may occur in response until successive years of increased population growth results in a substantial increase in abundance.

Table 2. Three indicators of adult delta smelt status for WYs 2002-2019. Column 2 is the CDFW FMWT Index by WY (i.e., the indices for calendar years (CY) 2001-2018). Column 3 is the CDFW SKT Index. Column 4 is an estimate of adult delta smelt abundance during January and February that the Service calculates from the SKT survey.

FMWT

SKT Index

January and February SKT Abundance WY Index

(unitless) Estimate (number of delta smelt)

(unitless) [Lower; Upper Confidence Interval]

2002 603 (CY 2001) NIA 739,877 [506,889; 1,043,891]

2003 13 9 (CY 2002) NIA 634,000 [340,811; 1,081,388]

2004 210 (CY 2003) 99.7 654,492 [370,200; 1,074,662]

2005 74 (CY 2004) 52.9 477,775 [308,015; 708,388]

2006 26 (CY 2005) 18.2 186,797 [133,663; 254,133]

2007 41 (CY 2006) 32.5 291,964 [155,148; 502,239]

2008 28 (CY 2007) 24.1 325,333 [147,533; 626,188]

2009 23 (CY 2008) 43.8 365,946 [151,439; 748,841]

2010 17 (CY 2009) 27.4 169,417 [106,837; 255,665]

2011 29 (CY 2010) 18.8 290,792 [99,502; 670,574]

2012 343 (CY 2011) 130.2 772,311 [420,904; 1,303,955]

2013 42 (CY 2012) 20.4 212,504 [95,804; 410,659]

2014 18 (CY 2013) 30.1 207,595 [110,373; 356,969]

2015 9 (CY 2014) 13.8 139,310 [66,314; 259,301]

2016 7 (CY 2015) 1.8 16,159 [7,403; 30,886]

2017 8 (CY 2016) 3.8 47,786 [21,709; 91,864]

2018 2 (CY 2017) 2.1 17,606 [3,433; 54,796]

2019 0 (CY2018) Pending Pending

In addition to these abundance estimates, the CDFW conducts four fish surveys from which it develops indices of delta smelt's relative abundance (Figures 4 and 5). Each survey has variable and unquantified capture efficiency, and in each, the frequency of zero catches of delta smelt is very high, largely due to the species' rarity (e.g., Latour 2016; Polansky et al. 2017). The [summer] Townet Survey (TNS) is the longest running indicator of delta smelt relative abundance; it has been conducted since 1959. Although this survey was designed to index the

Ms. Tessa E. Beach 8 relative abundance of metamorphosing juvenile striped bass (Marone saxatilis) (Turner and Chadwick 1972), delta smelt have been collected incidentally; most of the delta smelt captured are age-0 and about 20-40 mm in length (Miller 2000). The FMWT is the second longest running indicator of delta smelt relative abundance; it has been conducted since 1967. This survey was also designed to index the relative abundance of age-0 striped bass (Stevens 1977), but as with the TNS, delta smelt are collected incidentally (Stevens and Miller 1983). Most of the delta smelt captured by the FMWT are age-0 "subadults" and are about 50-70 mm in length (Sweetnam 1999). The 20-mm Survey is the third longest running indicator of delta smelt relative abundance; it has been conducted since 1995. This survey was designed to monitor the distribution of late larval or metamorphosing juvenile delta smelt to assess their distribution and risk of entrainment into the large water export diversions of the Central Valley Project (CVP) and State Water Project (SWP) (Dege and Brown 2004). As its name suggests, most of the delta smelt collected by the 20-mm Survey are about 10-30 mm in length, with a peak catch offish just under 20 mm (Kimmerer 2008). The newest indicator of delta smelt relative abundance is the SKT Survey, which has been conducted since 2002. This survey was designed to monitor the distribution of pre-spawn and spawning adult delta smelt to assess their distribution and risk of entrainment. Most of the delta smelt captured in the SKT are 60-80 mm in length (Bennett 2005).

The TNS and FMWT abundance indices for delta smelt have documented the species' long-term decline, while the newer 20-mm and SKT abundance indices have generally confirmed the recent portions of the trends implied by the older surveys (Figures 4 and 5). During the period ofrecord, juvenile delta smelt relative abundance has declined from peak levels observed during the latter 1970s (Figure 4), while subadult relative abundance was at its highest in 1970, and similarly high in 1980 (Figure 5). Juvenile and subadult abundance indices both declined rapidly during the early 1980s, increased somewhat during the 1990s, and then collapsed in the early 2000s. Since 2005, the TNS and the FMWT have produced indices that reflect less year to year variation than their 20-mm and SKT analogs, but overall, the trends in both sets of indices are similar. During the past decade, each index has frequently reached new record low levels. The TNS index was

0.0 in 2015 and 2016, and the 2015 FMWT index and subsequent 2016 SKT index were record lows ( about one half of one percent of the relative abundance recorded in 1970-1971 ).

1955 1965 1975 1985 Year

1995 2005

X

120 ~ C:

100 E E

80 I N

Figure 4. Time series of the CDFW's summer TNS (black line; primary y-axis) and 20-mm Survey (gray line; secondary y-axis) abundance indices for delta smelt.

X 1400 -Cb -a C

;: 1200

~ 1000 Cb 1u 800

I 600

3!. 400 \;

1965 1975 1985 1995 2005

Year

X Q)

500 -g 3::

400 ~ ro

300 ~

0.0

200 ·=

L a.

Vl

Figure 5. Time series of the CDFW's FMWT (black line; primary y-axis) and SKT (gray line;

secondary y-axis) abundance indices for delta smelt.

The abundance of adult delta smelt may have exceeded twenty million in 1980-1981 (Rose et al.

2013b). This may sound like a large number- and it is compared to the contemporary estimates listed in Table 2. However, decades of monitoring by CDFW has shown that the delta smelt has usually not been very abundant when compared to other pelagic (meaning offshore-oriented or open-water) fishes (Figure 6). In the TNS, delta smelt catches have usually been lower than age-0 striped bass, and in recent years, also lower than gobies and threadfin shad. In the FMWT, delta smelt catches have been persistently lower than at least five other species. Research and monitoring in shallower habitats like Suisun Marsh (Moyle et al. 1986; Matern et al. 2002), Delta beaches (Nobriga et al. 2005), and small tidal marshes in the upper estuary (Gewant and Bollens 2012) have reported even lower relative abundances of delta smelt. In each of the studies cited, the catches of delta smelt represented less than one percent of the total fish catch and there were usually more than a dozen more abundant fish species.

100%

.c 80% - I.I ..

60% RI

I.I

'6

40% QI

Ill)

RI

20% ..

C

QI

C,I .. 0% QI

A.

C"l

LO

CJ'\

..-t

■ Age-0S triped Bass

■ Delta Smelt

■ Northern Anchovy

Tridentiger spp_ a a ,..._ 00 m m ..-t ..-t a

CJ'\

CJ'\

..--I

Year

• American Shad

• Longfin Smelt

■ Threadfin Shad

"' Yellowfin Goby a a a ..-t a a N N

Summer Tow-net Survey

100%

80%

60%

40%

20%

0% I.() m ..-t

• Ame r K:an Shad

Longfin Smelt

■ Pac ific Herring

■ Threadlin Shad

00 ,..._ C"l ..-t m 00 m ..-t

■ Delta Smelt

■ Northern Anchovy

■ Striped Bass age-0

C"l m m ..-t m N

Fall MidwaterTrawl

Figure 6. Fractional compositions of the eight most frequently collected fish species in the CDFW's summer TNS (1959-2015), and the seven most frequently collected fish species in the FMWT (1967- 2015).

The long-term rarity of the delta smelt has had a consequence for understanding the reasons for their population decline, which generates uncertainty about how resource managers should intervene. Some pelagic fishes have shown long-term relationships between Delta inflow, Delta outflow and their abundance or survival (Stevens and Miller 1983; Jassby et al. 1995; Kimmerer 2002b; Kimmerer et al. 2009). There does seem to be some difference in the likelihood of whether the delta smelt population will increase or decrease in abundance from one year to the next based on hydrology (Figure 7), but there has never been any predictable relationship linking freshwater flow conditions to the relative abundance of delta smelt (Stevens and Miller 1983;

Jassby et al. 1995; Kimmerer 2002b; Kimmerer et al. 2009). Recently, several teams of researchers have built several varieties of conceptual (IEP 2015) and mathematical (Thomson et

al. 2010; Maunder and Deriso 2011; Miller et al. 2012; Rose et al. 2013a) life cycle models for the delta smelt that attempt to describe the reasons the population has declined. Some of these models have been able to recreate the trend observed in abundance indices very well (Figure 8), but they have all done so using different approaches and different variables. Collectively, these modeling efforts have been helpful in that they generally support water temperature and changes in the estuary's food web as 'universally supported' factors affecting delta smelt. However, they have also come to very different conclusions about the conservation value of more readily manageable factors like water project operations.

A I I

QJ u C:

~ 10 C:

:::J

-fil 't:J

3: 5 (1J

QJ

b

QJ u C:

(1J

't:J

§ -5 -fil 't:J

QJ

Ill m -10 b

QJ

I v -15

■ Up Maybe Up ■ Down ■ Maybe down

Wet or Above-normal Dry or Critica I

Figure 7. Frequencies of delta smelt population increases or decreases (red colored portions of each bar occurring below zero) based on the CDFW's FMWT Survey, 1967-2015. A population increase reflects an increase in relative abundance over the prior year's index and a population decrease reflects a decrease in relative abundance compared to the prior year's index. The Service performed bootstrap resampling on each year's catch per tow to generate a mean catch per tow with 95 percent confidence intervals. This resulted in four possible outcomes: (1) a statistically significant increase in relative abundance from one year to the next in which the confidence intervals of the two years did not overlap ("Up"; solid blue bar segments), (2) a statistically non-significant increase in relative abundance from one year to the next in which the confidence intervals of the two years overlapped ("Maybe Up"; lighter blue bar segments), (3) a statistically significant decrease in relative abundance from one year to the next in which the confidence intervals of the two years did not overlap ("Down"; solid red bar segments), or (4) a statistically non-significant decrease in relative abundance from one year to the next in which the confidence intervals of the two years overlapped ("Maybe Down"; lighter red bar segments). The counts in each of the four categories were combined by Sacramento Valley WY types except that below-normal years were not plotted.

The frequencies of population decline were converted into a negative number so that population increases would count up from the zero line on the y-axis and population decreases would count down from the zero line.

Maunder and Deriso {2011} lbl ...

I ' .. i :; • u ' I :~

J , .• o., " l<I r: I • J ,, I L,I mo

1070 ,.,.

Thomson et al. (2010}

Miller et al. {2012)

Year

IP07 1D !VA 2000 1001 l(lCQ' 1'XO 20l)I ~

Year

0.60 Q..

0.25 Q..

Rose et al. (2013a)

Figure 8. Examples of recent published model fits to time series of delta smelt relative abundance data. The source of each is referenced above or alongside each time series. In each plot, observed catches are depicted as black dots and model predictions of the data as gray or black lines. Model predictions from Rose et al. (2013a) are a black line with open symbols. In Maunder and Deriso (2011), the three panels represent the 20-mm Survey, summer TNS, and FMWT Survey from top to bottom, respectively. The other three studies are fit to estimates of adult delta smelt relative abundance (FMWT catch in Thomson et al. 2010 and the FMWT index in Miller et al 2012) or absolute abundance (Rose et al. 2013a). See each study for further details on Methods, Results, and the authors' interpretations of their results.

Habitat and Distribution

Because the delta smelt only lives in part of one comprehensively monitored estuary, its general distribution is well understood (Moyle et al. 1992; Bennett 2005; Hobbs et al. 2006, 2007; Feyrer et al. 2007; Nobriga et al. 2008; Kimmerer et al. 2009; Merz et al. 2011; Murphy and Hamilton 2013; Sommer and Mejia 2013). There are both location-based (e.g., Sacramento River around Decker Island) and conditions-based (low-salinity zone) habitats that delta smelt permanently occupy. There are habitats that delta smelt occupy seasonally (e.g., for spawning), and there are habitats that delta smelt occupy transiently, which we define here as occasional seasonal use.

These include distribution extremes from which delta smelt are not collected every year or even in most years.

Ms. Tessa E. Beach 13

Most delta smelt complete their entire life cycle within or immediately upstream of the estuary's low-salinity zone. The low-salinity zone is frequently defined as waters with a salinity range of about 0.5 to 6 parts per thousand (ppt) (Kimmerer 2004). The 0.5 to 6 ppt and similar salinity ranges reported by different authors were chosen based on analyses of historical peaks in phytoplankton and zooplankton abundance, but recent physiological and molecular biological research has indicated that the salinities that typify the low-salinity zone are also optimal for delta smelt (Komoroske et al. 2016). The low-salinity zone is a dynamic habitat with size and location that respond rapidly to changes in tidal and river flows. By local convention the location of the low-salinity zone is described as "X2" in terms of the distance from the 2 ppt isohaline to the Golden Gate Bridge. The U.S. Environmental Protection Agency (EPA) recently finished a comprehensive set of maps that show how the low-salinity zone changes in size and shape when freshwater flows change the location of X22

• The low-salinity zone expands and moves downstream when river flows into the estuary are high, placing low-salinity water over a larger and more diverse set of nominal habitat types than occurs under low flow conditions. During periods of low outflow, the low-salinity zone contracts and moves upstream. Due to its historical importance as a fish nursery habitat, there is a long research history into the physics and biology of the San Francisco Estuary's low-salinity zone (Kimmerer 2004).

The ecological function of the low-salinity zone also varies depending mainly on freshwater flow (Jassby et al. 1995; Kimmerer 2002a; Kimmerer 2004). Low outflow can decrease the capacity of the low-salinity zone and adjacent habitats to support the production of delta smelt by reducing habitat diversity and concentrating the fish with their predators and competitors (Service 1993, 1994). During the past four decades, the low-salinity zone ecosystem has undergone substantial changes in turbidity (Schoellhamer 2011) and food web function (Winder and Jassby 2011) that cannot be undone solely by increasing Delta outflow. These habitat changes, which extend into parts of the Delta where water is fresher than 0.5 ppt, have also decreased the ability of the low-salinity zone and adjacent habitats to support the production of delta smelt (Thomson et al. 2010; Rose et al. 2013b; IEP 2015).

Delta smelt have been observed as far west as San Francisco Bay, as far north as Knights Landing on the Sacramento River, as far east as Woodbridge on the Mokelumne River and Stockton on the Calaveras River, and as far south as Mossdale on the San Joaquin River. This distribution represents a range of salinity from essentially zero ppt up to about 20 ppt, which represents a salinity range well beyond definitions of the low salinity zone or mixing zone near a salinity of 2 ppt emphasized in the critical habitat rule (Service 1994 ). It is also well beyond the geographic extent of the critical habitat rule. However, most delta smelt that have been collected in the extensively surveyed San Francisco Estuary have been collected from locations within the bounds defined in the critical habitat rule. In addition, all habitats known to be occupied year around by delta smelt occur within the bounds defined in the critical habitat rule.

Delta smelt permanently occupy the Cache Slough 'Complex', including Liberty Island and the adjacent reach of the Sacramento Deepwater Shipping Channel (Sommer and Mejia 2013), Cache Slough to its confluence with the Sacramento River and the Sacramento River from that confluence downstream to Chipps Island, Honker Bay, and the eastern part of Montezuma Slough (Figure 6). The reasons delta smelt are believed to permanently occupy this part of the estuary are the year-round presence of fresh- to low-salinity water that is comparatively turbid

2http://www.waterboards.ca.gov/waterrights/water _issues/programs/bay_ Delta/docs/cmnt081712/karen _ schwinn.pdf

Ms. Tessa E. Beach 14 and of a tolerable water temperature. These appropriate water quality conditions overlap an underwater landscape featuring variation in depth, tidal current velocities, edge habitats, and food production (Sweetnam 1999; Nobriga et al. 2008; Feyrer et al. 2011; Murphy and Hamilton 2013; Hammock et al. 2015; Bever et al. 2016). Field observations are increasingly supported by laboratory research that explains how delta smelt respond physiologically to variation in salinity, turbidity, water temperature, and other aspects of their habitat that can vary with changes in climate, freshwater flow and estuarine bathymetry (Hasenbein et al. 2014; 2016; Komoroske et

al. 2014; 2016).

Each year, the distribution of delta smelt seasonally expands when adults disperse in response to winter flow increases that also coincide with seasonal increases in turbidity and decreases in water temperature (Figure 9). The annual range expansion of adult delta smelt extends up the Sacramento River to about Garcia Bend in the Pocket neighborhood of Sacramento, up the San Joaquin River from Antioch to areas near Stockton, up the lower Mokelumne River system, and west throughout Suisun Bay and Suisun Marsh. Some delta smelt seasonally and transiently occupy Old and Middle river in the south Delta each year, but face a high risk of entrainment when they do (Grimaldo et al. 2009).

f Adults in kodiak trawls sampling offshore surface waters, January-May

Larvae in 20-mm trawls sampling offshore

Adults in beach seines sampling very close to shorelines, March-April

Juveniles in midwater trawls sampling offshore water columns, September December

Figure 9. Maps of multi-year average distributions of delta smelt collected in four monitoring programs. The sampling regions covered by each survey are outlined. The areas with dark shading surround sampling stations in which 90 percent of the delta smelt collections occurred, the areas with light shading surround sampling stations in which the next 9 percent of delta smelt collections occurred. Source: Murphy and Hamilton (2013).

Ms. Tessa E. Beach 15

The distribution of delta smelt occasionally expands beyond this area (Figure 6). For instance, during high outflow winters, adult delta smelt also disperse west into San Pablo Bay and up into the Napa River (Hobbs et al. 2007). Similarly, delta smelt have occasionally been reported from the Sacramento River north of Garcia Bend up to Knights Landing ( e.g., Merz et al. 2011; Vincik and Julienne 2012).

The expanded adult distribution initially affects the distribution of the next generation because delta smelt eggs are adhesive and not believed to be highly mobile once they are spawned. The distribution of larvae reflects a combination of where spawning occurred and freshwater flow conditions when the eggs hatched. Variation in Delta outflow affects the spatial distribution of the delta smelt population for most of its life. The ecological condition of the estuary's low salinity zone has historically been indexed using a statistic called X2, a local name for the geographic location of2 ppt salinity near the bottom of the water column (Jassby et al. 1995).

During spring, larval delta smelt have centers of distribution in freshwater, typically 20-40 km upstream ofX2 (Dege and Brown 2004). By July, as water temperatures in the Delta reach annual peaks, post-larval and juvenile delta smelt have centers of distribution very close to X2 (Dege and Brown 2004), but the fish are broadly distributed around that peak (Sweetnam 1999;

Nobriga et al. 2008). During the fall, subadult delta smelt still have a center of distribution near X2 (Sommer et al. 2011), and remain broadly distributed around that peak (Feyrer et al. 2007;

2011). During the winter, maturing adult delta smelt disperse in connection with winter storms following the spread of turbid freshwater (Grimaldo et al. 2009; Sommer et al. 2011; Murphy and Hamilton 2013). Recent analyses suggest that after an initial dispersal in December, the adult delta smelt population does not respond strongly to variation in Delta outflow during January to May (Polansky et al. 2017), though some individuals continue to move around in response to flow changes associated with storms (Polansky, unpublished analysis of Early Warning Survey data set).

Food

At all life stages, numerous small planktonic crustaceans, especially a group called calanoid copepods, make up most of the delta smelt diet (Nobriga 2002; Slater and Baxter 2014). Small crustaceans are ubiquitously distributed throughout the estuary, but which prey species are present at particular times and locations has changed dramatically over time (Winder and Jassby 2011; Kratina et al. 2014 ). This has likely affected delta smelt feeding success, particularly during Central California's warm summers.

Reproductive Strategy

The reproductive behavior of delta smelt is only known from captive specimens spawned in artificial environments and most of the information has never been published. Spawning likely occurs mainly at night with several males attending a female that broadcasts her eggs onto bottom substrate (Bennett 2005). Although preferred spawning substrate is unknown, spawning habits of delta smelt's closest relative, the surf smelt (Hypomesus pretiosus), as well as unpublished experimental trials, suggest that sand may be the preferred substrate (Bennett 2005).

Hatching success peaks at temperatures of l 5- l 6°C ( 59-61 °F) and decreases at cooler and warmer temperatures. Hatching success nears zero percent as water temperatures exceed 20°C (68°F) (Bennett 2005). Water temperatures suitable for spawning occur most frequently during the months of March-May, but ripe female delta smelt have been observed as early as January and larvae have been collected as late as July.

Delta smelt spawn in the estuary and have one spawning season for each generation, which makes the timing and duration of the spawning season important every year. As stated above, delta smelt are believed to spawn on sandy substrates in fresh and possibly low-salinity water (Bennett 2005). Therefore, freshwater flow affects how much of the estuary is available for delta smelt to spawn (Hobbs et al. 2007).

Delta smelt can start spawning when water temperatures reach about 10°C (50°F) and can continue until temperatures reach about 20°C (Bennett 2005). The ideal spawning condition occurs when water temperatures remain cool throughout the spring (e.g., March-May). Few delta smelt :'.S 55 mm in length are sexually mature and 50% of delta smelt reach sexual maturity at 60 to 65 mm in length (Rose et al. 2013b). Thus, if water temperatures rise much above 10°C in the winter, the "spawning season" can start before most individuals are mature enough to actually spawn. If temperatures continue to warm rapidly toward 20°C in early spring, that can end the spawning season with only a small fraction of 'adult' fish having had an opportunity to spawn.

Delta smelt were initially believed to spawn only once before dying (Moyle et al. 1992). It has since been confirmed that like many other ecologically similar forage fishes (Winemiller and Rose 1992), individual delta smelt can spawn more than once if water temperatures remain suitable for a sufficient length of time, and if the adults find enough food to support the production of another batch of eggs (Lindberg et al. 2013; Kurobe et al. 2016). As a result, the longer water temperatures remain cool, the more fish have time to mature and the more times individual fish can spawn.

Although adult delta smelt can spawn more than once, mortality is high during the spawning season and most adults die by May (Polansky et al. 201 7). The egg stage averages about 10 days before the embryos hatch into larvae. The larval stage averages about 30 days. Metamorphosing "post-larvae" appear in monitoring surveys from April into July of most years. By July, most delta smelt have reached the juvenile life stage. Delta smelt collected during the fall are called "subadults", a stage which lasts until winter when fish disperse toward spawning habitats. This winter dispersal usually precedes sexual maturity (Sommer et al. 2011).

Recovery and Management

Following Moyle et al. (1992), the Service (1993) indicated that SWP and CVP exports were the primary factors contributing to the decline of delta smelt due to entrainment of larvae and juveniles and the effects of low flow on the location and function of the estuary mixing zone ( now called the low-salinity zone). In addition, prolonged drought during 1987-1992, in-Delta water diversions, reduction in food supplies by nonindigenous aquatic species, specifically overbite clam and nonnative copepods, and toxicity due to agricultural and industrial chemicals were also factors considered to be threatening the delta smelt. In the 2008 Service biological opinion on the CVP and SWP operations (2018 Service BiOP), the Service's Reasonable and Prudent Alternative required protection of delta smelt from entrainment in December through June and augmentation of Delta outflow during the fall of Wet or Above-Normal years as classified by the State of California (Service 2008). The expansion of entrainment protection for delta smelt in the 2008 Service BiOp was in response to large increases in juvenile and adult salvage in the early 2000s (Kimmerer 2008). The fall X2 requirement was in response to

Ms. Tessa E. Beach 17 increased fall exports that had resulted in greatly reduced variability in Delta outflow during the fall months (Feyrer et al. 2011 ).

Consistent with the 2008 Service BiOp, the Service's (2010c) recommendation to uplist delta smelt from threatened to endangered included reservoir operations and water diversions upstream of the estuary as mechanisms interacting with exports to restrict the low-salinity zone and concentrate delta smelt with competing fish species. In addition, Brazilian waterweed (Egeria densa) and increasing water transparency were considered new detrimental habitat changes.

Predation was considered a low-level threat linked to increasing waterweed abundance and increasing water transparency. Additional threats considered potentially significant by the Service in 2010 were entrainment into power plant diversions, contaminants, and reproductive problems that can stem from small population sizes. Conservation recommendations included:

establish Delta outflows proportionate to unimpaired flows to set outflow targets as fractions of runoff in the Central Valley watersheds; minimize reverse flows in Old and Middle river; and, establish a genetic management plan with the goals of minimizing the loss of genetic diversity and limiting risk of extinction caused by unpredictable catastrophic events. The Service (2012b) added climate change to the list of threats to the delta smelt.

Continued protection of the delta smelt from excessive entrainment, improving the estuary's flow regime, suppression of nonnative species, increasing zooplankton abundance, and improving water quality are among the actions needed to recover the delta smelt.

Climate Change

Climate projections for the San Francisco Bay-Delta and its watershed indicate that temperature and precipitation changes will diminish snowpack in the Sierra-Nevada, changing the timing and availability of natural water supplies (Knowles and Cayan 2002; Dettinger 2005). Warming may result in more precipitation falling as rain which will mean less water stored in spring ' snowpacks. This would increase the frequency of rain-on-snow events and increase winter runoff with an associated decrease in runoff for the remainder of the year (Hayhoe et al. 2004). Overall, these and other storm track changes may lead to increased frequency of flood and drought cycles during the 21 st century (Dettinger et al. 2015). Thus far, the 21 st century has been substantially drier than the 20th century (Figure 10) to which the frequency of WY type classifications are compared.

Sea level rise is also anticipated as a consequence of a warming global climate and if it is not mitigated, sea level rise will likely influence saltwater intrusion into the Bay-Delta. Salinity within the northern San Francisco Bay is projected to rise by 4.5 ppt by the end of the century (Cloern et al. 2011 ). Elevated salinity could push X2 further eastward in the estuary if outflows are not increased to compensate. Fall X2 mean values are projected to increase by about 7 km to the area near the City of Antioch approximately 90 km from the Golden Gate Bridge by 2100 (Brown et al. 2013). This projected change in the location of X2 in the fall is expected to decrease suitable physical habitat if current levees and channel structures are maintained.

Central California's warm summers are already a source of energetic stress for delta smelt and warm springs already severely compress the duration of their spawning season (Rose et al.

2013a,b). Central California's climate is anticipated to get warmer (Dettinger 2005). We expect warmer estuary temperatures to present a significant conservation challenge for delta smelt.

Ms. Tessa E. Beach 18

Mean annual water temperatures within the Delta are expected to increase steadily during the second half of this century (Cloem et al. 2011). Warmer water temperatures could further reduce delta smelt spawning opportunities, decrease juvenile growth during the warmest months, and increase mortality via several food web pathways including: increased vulnerability to predators, increased vulnerability to toxins, and decreased capacity for delta smelt to successfully compete in an estuary that is energetically more optimal for warm-water tolerant fishes.

■ 1906-1999 ■ 2000-2017

0.4

0.35

0.3 ro 0 0.25

C 0.2 ·p u 0.15 u..

0.1

0.05

Wet AN BN Dry Critical

Sacramento Valley Water Year Type

Figure 10. Frequency distribution of Sacramento Valley WY types for: blue==1906-1999 and red==2000-2017.

Recent research into the ecological effects of warming water temperatures suggests that delta smelt, depending on location, may be forced to spawn an average often to twenty-five days earlier in the season (Brown et al. 2013). The number of high mortality days (cumulative number of days of daily average water temperature >25°C (77°F) is expected to increase (Brown et al.

2013 ). The number of physiologically stressful days ( cumulative number of days of daily average water temperature >20°C (68°F)) is expected to be stable or decrease partly because many stressful days will become high mortality days. Thus, current modeling indicates that delta smelt will likely face a shorter maturation window and reduced habitat availability due to increased water temperatures. A shorter maturation window will likely have effects on reproduction (Brown et al. 2013). Growth rates have been shown to slow as water temperatures increase above 20°C (68°F), requiring delta smelt to consume more food to reach growth rates that are normal at lower water temperatures (Rose et al. 2013a). Delta smelt are smaller, on average, than in the past (Sweetnam 1999; Bennett 2005) and expected temperature increases due to climate change will likely slow growth rates further.

Ms. Tessa E. Beach 19

In summary, the delta smelt is currently at the southern limit of the inland distribution of the family Osmeridae along the Pacific coast of North America. Thus, increased temperatures associated with climate change may present a significant conservation challenge if they result in a Bay-Delta that is outside of the delta smelt's competitive limits. For the time being however, water temperatures are cool enough in the delta smelt's range for the species to complete its life cycle.

Summary of the Status of Delta Smelt

The relative abundance of delta smelt has reached very low numbers for a small forage fish in an ecosystem the size of the San Francisco Estuary. The extremely low recent relative abundance reflects decades of habitat change and marginalization by non-native species that prey on and out-compete delta smelt. The anticipated effects of climate change on the San Francisco Estuary and watershed such as warmer water temperatures, greater salinity intrusion, lower snowpack contribution to spring outflows from the Delta, and the potential for frequent extreme drought, which has been experienced for the 21 st century thus far (Figure 10) indicate challenges to delta smelt survival will increase. A rebound in relative abundance during the very wet and cool conditions during 2011 indicated that delta smelt retained some population resilience (IEP 2015).

However, since 2012, declines to record low population estimates have been broadly associated with the remarkably dry hydrology occurring from 2012 to 2016.

Environmental Baseline in the Action Area

The project occurs within Suisun Bay and adjacent sloughs, within the range of delta smelt. Delta smelt are located in the Suisun Bay year-round and are known to utilize the action area as habitat.

The project also occurs within the low salinity zone (LSZ) where smelt are known to rear, feed and breed. The Suisun Bay and the Confluence of the Sacramento and San Joaquin Rivers are considered critical areas within delta smelt habitat and the San Francisco Bay Estuary for the survival of this species. Delta smelt are often observed in the highest densities in these areas (Merz et al. 2011).

As detailed in the Status of the Species section of this biological opinion, the delta smelt abundance is at its historical low. The latest surveys to detect delta smelt within Suisun Bay were the Service's Enhanced Delta Smelt Monitoring Survey, which encountered one delta smelt this January. These studies monitor the juvenile and adult delta smelt distribution and relative abundance throughout their historical spring range in the Sacramento-San Joaquin Delta and San Francisco Estuary. It can be anticipated that delta smelt will be in the juvenile and subadult lifestages and located in the action area during the duration of the proposed project.